[DO NOT MERGE] stash: state of SILO executable for DEMO

[gordonkoehn]

This PR / branch contains the executable written by @Taepper for the first POC for importing V-Pipe's outputs into SILO.

This is the state of the 16.12.2024.

The entire code to execute and run SILO standalone with downloading data from the running

wise-seq.loculus.org demo instance.

[gordonkoehn]

This is the wrong version. To be updated by. @Taepper. Also, it misses an empty directory called silo_output.

[gordonkoehn]

Thanks for uploading !

[gordonkoehn]

Info to recall:

• state of SILO and LAPIS is in /ww_test
• ./run.bash : lädt alle Daten von der Loculus Instanz herunter, baut die Indexe und startet SILO
• docker compose up : startet die LAPIS api, welche das davor gestartete SILO aufruft

[Taepper]

Info to recall:

• state of SILO and LAPIS is in /ww_test
• ./run.bash : lädt alle Daten von der Loculus Instanz herunter, baut die Indexe und startet SILO
• docker compose up : startet die LAPIS api, welche das davor gestartete SILO aufruft

Oh, not quite anymore. You cited the instructions for a previous version of the demo. The up-to-date instructions are in ww_test/README.md:

To generate the input data run `./generate_silo_input.bash`.

This downloads all data from the loculus instance wise-seqs.loculus.org,
looks at the short-read s3Link, downloads all s3 buckets where the file 
ends with .ndjson.bz2 and merges them into a single .ndjson file.

To build the indexes and start the api, run `LAPIS_PORT=8080 docker compose up` where 
you can replace the `LAPIS_PORT`.

This builds the SILO indexes (service `siloPreprocessing`), 
starts the silo api (service `silo`) and the LAPIS api (service `lapis`).

[gordonkoehn]

Thanks for updating!